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article stringlengths 4.36k 149k | summary stringlengths 32 3.35k | section_headings listlengths 1 91 | keywords listlengths 0 141 | year stringclasses 13
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|---|---|---|---|---|---|
The Huntington's disease ( HD ) CAG repeat , encoding a polymorphic glutamine tract in huntingtin , is inversely correlated with cellular energy level , with alleles over ∼37 repeats leading to the loss of striatal neurons . This early HD neuronal specificity can be modeled by respiratory chain inhibitor 3-nitropropion... | Huntington's disease ( HD ) is a tragic neurodegenerative disorder caused by a CAG repeat that specifies the size of a glutamine tract in the huntingtin protein , such that the longer the tract , the earlier the loss of striatal brain cells . A correlation of polyglutamine tract size has also implicated huntingtin in t... | [
"Abstract",
"Introduction",
"Result/Discussion",
"Materials",
"and",
"Methods",
"Supporting",
"Information"
] | [
"mus",
"(mouse)",
"genetics",
"and",
"genomics"
] | 2007 | Unbiased Gene Expression Analysis Implicates the huntingtin Polyglutamine Tract in Extra-mitochondrial Energy Metabolism |
The intestinal microbiota enhances dietary energy harvest leading to increased fat storage in adipose tissues . This effect is caused in part by the microbial suppression of intestinal epithelial expression of a circulating inhibitor of lipoprotein lipase called Angiopoietin-like 4 ( Angptl4/Fiaf ) . To define the cis-... | Recent studies have revealed that the community of microorganisms residing in the intestine regulates fat storage . Microbes evoke this response in part by suppressing expression of the Angptl4 gene , which encodes a secreted inhibitor of fat storage . Although Angptl4 is expressed in multiple tissues , microbial suppr... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"microbiology",
"anatomy",
"and",
"physiology",
"animal",
"models",
"physiological",
"processes",
"developmental",
"biology",
"model",
"organisms",
"nutrition",
"gastroenterology",
"and",
"hepatology",
"aquaculture",
"molecular",
"genetics",
"gene",
"expression"... | 2012 | Intronic Cis-Regulatory Modules Mediate Tissue-Specific and Microbial Control of angptl4/fiaf Transcription |
Tumor cells do not develop in isolation , but co-evolve with stromal cells and tumor-associated immune cells in a tumor microenvironment mediated by an array of soluble factors , forming a complex intercellular signaling network . Herein , we report an unbiased , generic model to integrate prior biochemical data and th... | Tumor cells do not develop in isolation , but co-evolve with stromal cells via an array of soluble mediators . Here we report a model to integrate prior biochemical data and construct a glioma microenvironment in silico , which comprises 5 types of cells , 15 cytokines , and 69 signaling pathways . We observed a transi... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"biology",
"computational",
"biology"
] | 2012 | In silico Experimentation of Glioma Microenvironment Development and Anti-tumor Therapy |
Bardet-Biedl syndrome , BBS , is a rare autosomal recessive disorder with clinical presentations including polydactyly , retinopathy , hyperphagia , obesity , short stature , cognitive impairment , and developmental delays . Disruptions of BBS proteins in a variety of organisms impair cilia formation and function and t... | Bardet-Biedl syndrome , BBS , is a rare human genetic disease caused by mutations in many genes . The BBS phenotype is very complex; it is principally characterized by early-onset obesity , progressive blindness , extra digits on the hands and feet , and renal problems . BBS patients may also suffer from developmental ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"behavioral",
"neuroscience",
"model",
"organisms",
"genetics",
"biology",
"genetics",
"of",
"disease",
"neuroscience",
"genetics",
"and",
"genomics"
] | 2011 | Hyperactive Neuroendocrine Secretion Causes Size, Feeding, and Metabolic Defects of C. elegans Bardet-Biedl Syndrome Mutants |
To faithfully encode mechanosensory information , auditory/vestibular hair cells utilize graded synaptic vesicle ( SV ) release at specialized ribbon synapses . The molecular basis of SV release and consequent recycling of membrane in hair cells has not been fully explored . Here , we report that comet , a gene identif... | Ribbon synapses are found in the ear and eye and facilitate the transmission of sensory information to the brain . In hair cells of the ear , the molecules required for ribbon function have not been fully explored . Zebrafish are ideal for investigating molecular components of these specialized synapses because of the ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/animal",
"genetics",
"physiology/sensory",
"systems",
"neuroscience/sensory",
"systems"
] | 2009 | synaptojanin1 Is Required for Temporal Fidelity of Synaptic Transmission in Hair Cells |
During ischemic stroke , occlusion of the cerebrovasculature causes neuronal cell death ( infarction ) , but naturally occurring genetic factors modulating infarction have been difficult to identify in human populations . In a surgically induced mouse model of ischemic stroke , we have previously mapped Civq1 to distal... | Stroke is the second leading cause of death and the most common cause of acquired adult disability worldwide . Ischemic stroke is caused by an interruption of blood flow in the cerebral arteries and results in neuronal damage ( infarct ) to the area of perfusion in the brain . Although significant progress has been mad... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | Natural Genetic Variation of Integrin Alpha L (Itgal) Modulates Ischemic Brain Injury in Stroke |
Peripheral insulin resistance contributes to the development of type 2 diabetes . TCF7L2 has been tightly associated with this disease , although the exact mechanism was largely elusive . Here we propose a novel role of TCF7L2 in hepatic glucose metabolism in mammals . Expression of medium and short isoforms of TCF7L2 ... | Previous genome-wide association studies revealed that TCF7L2 is a strong candidate for a type 2 diabetes gene . However , the direct involvement of TCF7L2 on hepatic glucose metabolism has been elusive to date . Here we show that TCF7L2 is critical in mediating transcriptional control of hepatic glucose production . W... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"carbohydrate",
"metabolism",
"diabetes",
"mellitus",
"type",
"2",
"diabetic",
"endocrinology",
"dna",
"transcription",
"animal",
"models",
"model",
"organisms",
"metabolic",
"pathways",
"gene",
"expression",
"endocrinology",
"diabetes",
"and",
"endocrinology"... | 2012 | TCF7L2 Modulates Glucose Homeostasis by Regulating CREB- and FoxO1-Dependent Transcriptional Pathway in the Liver |
Minor histocompatibility ( H ) antigens are allogeneic target molecules having significant roles in alloimmune responses after human leukocyte antigen–matched solid organ and stem cell transplantation ( SCT ) . Minor H antigens are instrumental in the processes of transplant rejection , graft-versus-host disease , and ... | Peptides from cellular proteins evoking alloimmune responses in human leukocyte antigen–identical transplantation are called minor histocompatibility ( H ) antigens . Upon hematopoietic stem cell transplantation ( HSCT ) for hematological malignancies or for solid tumors , responses to minor H antigens may have detrime... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods",
"Supporting",
"Information"
] | [
"oncology",
"homo",
"(human)",
"hematology",
"immunology"
] | 2007 | Phenotype Frequencies of Autosomal Minor Histocompatibility Antigens Display Significant Differences among Populations |
Zoonotic disease ( ZD ) pose a serious threat to human health in low-income countries . In these countries the human burden of disease is often underestimated due to insufficient monitoring because of insufficient funding . Quantification of the impact of zoonoses helps in prioritizing healthcare needs . Kyrgyzstan is ... | Zoonoses are diseases transmitted from vertebrate animals to humans . They can cause a variety of symptoms ranging from mild gastrointestinal complaints to debilitating illness and even death . Especially in low-income countries where animals play an important role for many , the burden of these diseases can be substan... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"tropical",
"diseases",
"parasitic",
"diseases",
"salmonellosis",
"brucellosis",
"bacterial",
"diseases",
"rabies",
"neglected",
"tropical",
"diseases",
"veterinary",
"science",
"campylobacteriosis",
"echinococcosis",
"public",
"and"... | 2016 | The Burden of Zoonoses in Kyrgyzstan: A Systematic Review |
Foci of the HIV epidemic and helminthic infections largely overlap geographically . Treatment options for helminth infections are limited , and there is a paucity of drug-development research in this area . Limited evidence suggests that antiretroviral therapy ( ART ) reduces prevalence of helminth infections in HIV-in... | The geographical distribution of helminth infections , which are highly prevalent in many areas , overlaps considerably with regions of high HIV sero-prevalence . The highest burden of infection is found in resource-poor settings , making it unattractive for the pharmaceutical industry to invest . Limited available tre... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Impact of Anti-Retroviral Treatment and Cotrimoxazole Prophylaxis on Helminth Infections in HIV-Infected Patients in Lambaréné, Gabon |
Mouse Zfy1 and Zfy2 encode zinc finger transcription factors that map to the short arm of the Y chromosome ( Yp ) . They have previously been shown to promote meiotic quality control during pachytene ( Zfy1 and Zfy2 ) and at the first meiotic metaphase ( Zfy2 ) . However , from these previous studies additional roles f... | The mouse Y chromosome genes Zfy1 and Zfy2 were first identified in the late 1980s during the search for the gene on the Y that triggers male development; they encode proteins that regulate the expression of other genes to which they bind via a ‘zinc finger’ domain . We have now discovered that these genes play importa... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"meiosis",
"cell",
"biology",
"cell",
"cycle",
"and",
"cell",
"division",
"genetics",
"biology",
"and",
"life",
"sciences",
"cell",
"processes",
"molecular",
"cell",
"biology",
"gene",
"function"
] | 2014 | Mouse Y-Linked Zfy1 and Zfy2 Are Expressed during the Male-Specific Interphase between Meiosis I and Meiosis II and Promote the 2nd Meiotic Division |
The mismatch negativity ( MMN ) is a differential brain response to violations of learned regularities . It has been used to demonstrate that the brain learns the statistical structure of its environment and predicts future sensory inputs . However , the algorithmic nature of these computations and the underlying neuro... | The ability to predict one's environment is crucial for adaptive and proactive behaviour . It requires learning a mental model that captures the environment's statistical regularities . A process of this sort is thought to be reflected by the mismatch negativity ( MMN ) potential , a non-invasive electrophysiological m... | [
"Abstract",
"Introduction",
"Models",
"and",
"Methods",
"Results",
"Discussion"
] | [
"computational",
"neuroscience",
"biology",
"neuroscience"
] | 2013 | Modelling Trial-by-Trial Changes in the Mismatch Negativity |
Strongyloides stercoralis is a soil-transmitted nematode that can replicate within its host , leading to long-lasting and potentially fatal infections . It is ubiquitous and highly prevalent in Cambodia . The extent of morbidity associated with S . stercoralis infection is difficult to assess due to the broad spectrum ... | Strongyloides stercoralis is an intestinal parasite that infects humans by penetrating intact skin . It thrives particularly in tropical countries with poor sanitation . Because it can replicate within its host , it causes long-lasting infections and is potentially fatal in patients with a disseminated infection . S . ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"dermatology",
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"respiratory",
"infections",
"urticaria",
"helminths",
"parasitic",
"diseases",
"animals",
"pulmonology",
"strongyloides",
"stercoralis",
"strongyloides",
"parasitic",
"intestinal",
"diseases",
"protozoa... | 2017 | Strongyloides stercoralis is associated with significant morbidity in rural Cambodia, including stunting in children |
All organisms wishing to survive and reproduce must be able to respond adaptively to a complex , changing world . Yet the computational power available is constrained by biology and evolution , favouring mechanisms that are parsimonious yet robust . Here we investigate the information carried in small populations of vi... | A general problem in neuroscience is understanding how sensory systems organise information to be at the service of behaviour . Computational approaches can be useful for such studies as they allow one to simulate the sensory experience of a behaving animal whilst considering how sensory information should be encoded .... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"pattern",
"recognition",
"receptors",
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"immunology",
"social",
"sciences",
"neuroscience",
"animals",
"artificial",
"neural",
"networks",
"animal",
"models",
"drosophila",
"melanogaster",
"model",
"organisms",
"cog... | 2017 | Neural coding in the visual system of Drosophila melanogaster: How do small neural populations support visually guided behaviours? |
Host-range shifts in influenza virus are a major risk factor for pandemics . A key question in the study of emerging zoonoses is how the evolution of transmission efficiency interacts with heterogeneity in contact patterns in the new host species , as this interplay influences disease dynamics and prospects for control... | Influenza virus infects a range of vertebrate hosts , including domesticated animals as well as humans . Some of the most serious influenza pandemics in humans have involved host range shifts , when an influenza virus jumps from one host species to another . Importantly , however , host range shifts do not always cause... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"systems",
"biology",
"systems",
"ecology",
"medicine",
"and",
"health",
"sciences",
"veterinary",
"epidemiology",
"ecology",
"evolutionary",
"biology",
"population",
"modeling",
"epidemiology",
"population",
"dynamics",
"biology",
"and",
"life",
"sciences",
"population",... | 2014 | Contact Heterogeneity, Rather Than Transmission Efficiency, Limits the Emergence and Spread of Canine Influenza Virus |
Influenza A virus ( IAV ) enters host cells upon binding of its hemagglutinin glycoprotein to sialylated host cell receptors . Whereas dynamin-dependent , clathrin-mediated endocytosis ( CME ) is generally considered as the IAV infection pathway , some observations suggest the occurrence of an as yet uncharacterized al... | Attachment to and entry into a host cell are the first crucial steps in establishing a successful virus infection and critical factors in determining host cell and species tropism . Influenza A virus ( IAV ) attaches to host cells by binding of its major surface protein , hemagglutinin , to sialic acids that are omnipr... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Material",
"and",
"Methods"
] | [
"virology/host",
"invasion",
"and",
"cell",
"entry",
"virology"
] | 2011 | Dissection of the Influenza A Virus Endocytic Routes Reveals Macropinocytosis as an Alternative Entry Pathway |
Vector competence of Aedes aegypti mosquitoes is a quantitative genetic trait that varies among geographic locations and among different flavivirus species and genotypes within species . The subspecies Ae . aegypti formosus , found mostly in sub-Saharan Africa , is considered to be refractory to both dengue ( DENV ) an... | Vector competence is defined as the intrinsic permissiveness of an arthropod vector for infection , dissemination , and transmission of a pathogen . The mosquito Aedes aegypti is the main vector for dengue and yellow fever viruses worldwide and is divided into two subspecies: Ae . aegypti aegypti and Ae . aegypti formo... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"ecology",
"biology",
"and",
"life",
"sciences",
"population",
"biology",
"species",
"interactions",
"microbiology"
] | 2014 | Vector Competence in West African Aedes aegypti Is Flavivirus Species and Genotype Dependent |
In the bacterial world , methylation is most commonly associated with restriction-modification systems that provide a defense mechanism against invading foreign genomes . In addition , it is known that methylation plays functionally important roles , including timing of DNA replication , chromosome partitioning , DNA r... | DNA methylation in bacteria plays important roles in cell division , DNA repair , regulation of gene expression , and pathogenesis . Here , we use a novel sequencing technique , Single-Molecule Real-Time ( SMRT ) sequencing , to determine the methylomes of two related human pathogen species , Mycoplasma genitalium G-37... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"microbiology",
"dna",
"transcription",
"genome",
"sequencing",
"epigenetics",
"chromosome",
"biology",
"gene",
"expression",
"microbial",
"pathogens",
"comparative",
"genomics",
"biology",
"dna",
"modification",
"systems",
"biology",
"genetics",
"genomics",
"genetics",
"... | 2013 | Comprehensive Methylome Characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at Single-Base Resolution |
Pathogenic mechanisms of Candida glabrata in oral candidiasis , especially because of its inability to form hyphae , are understudied . Since both Candida albicans and C . glabrata are frequently co-isolated in oropharyngeal candidiasis ( OPC ) , we examined their co-adhesion in vitro and observed adhesion of C . glabr... | Understanding how Candida glabrata is able to establish oral mucosal infections is particularly important since many C . glabrata strains are innately resistant to azole antifungal drugs used in treating mucosal and disseminated infections . The epidemiology of C . glabrata oral infections shows that C . glabrata is ve... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"bacteriology",
"biofilms",
"cell",
"walls",
"medicine",
"and",
"health",
"sciences",
"yeast",
"infections",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"microbiology",
"fungi",
"model",
"organisms",
"tongue",
"fungal",
"diseases",
"cellular",
"structures... | 2016 | Candida glabrata Binding to Candida albicans Hyphae Enables Its Development in Oropharyngeal Candidiasis |
We present 10 tips for building effective lessons that are grounded in empirical research on pedagogy and cognitive psychology and that we have found to be practically useful in both classroom and free-range settings
There are many kinds of lessons , both formal and informal , from seconds long to lifelong . Most peopl... | As a species , we know as much about teaching and learning as we do about public health , but most people who teach at the postsecondary level are never introduced to even the basics of evidence-based pedagogy . Knowing just a few key facts will help you build more effective lessons in less time and with less pain and ... | [
"Abstract",
"Introduction",
"1.",
"Use",
"learner",
"personas",
"to",
"define",
"your",
"audience",
"2.",
"Design",
"for",
"effective",
"learning",
"strategies",
"3.",
"Write",
"summative",
"assessments",
"to",
"set",
"concrete",
"goals",
"4.",
"Write",
"formative... | [
"learning",
"neurolinguistics",
"linguistics",
"education",
"social",
"sciences",
"neuroscience",
"learning",
"and",
"memory",
"cognitive",
"psychology",
"cognition",
"memory",
"vision",
"cognitive",
"linguistics",
"instructors",
"human",
"learning",
"memory",
"recall",
"... | 2019 | Ten quick tips for creating an effective lesson |
The CDKN1B gene encodes the cyclin-dependent kinase inhibitor p27KIP1 , an atypical tumor suppressor playing a key role in cell cycle regulation , cell proliferation , and differentiation . Impaired p27KIP1 expression and/or localization are often observed in tumor cells , further confirming its central role in regulat... | Gene expression can be modulated at different steps on the way from DNA to protein including control of transcription , translation , and post-translational modifications . An abnormality in the regulation of mRNA and protein expression is a hallmark of many human diseases , including cancer . In some eukaryotic genes ... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"genetic",
"mutation",
"gene",
"regulation",
"mutation",
"types",
"molecular",
"genetics",
"gene",
"expression",
"endocrinology",
"diabetes",
"and",
"endocrinology",
"biology",
"autosomal",
"dominant",
"protein",
"translation",
"genetics",
"human",
"genetics",... | 2013 | A Novel Mutation in the Upstream Open Reading Frame of the CDKN1B Gene Causes a MEN4 Phenotype |
The pigment cells of vertebrates serve a variety of functions and generate a stunning variety of patterns . These cells are also implicated in human pathologies including melanoma . Whereas the events of pigment cell development have been studied extensively in the embryo , much less is known about morphogenesis and di... | Understanding the biology of post-embryonic stem and progenitor cells is of both basic and translational importance . To identify mechanisms by which stem and progenitor cells are established , maintained , and recruited to particular fates , we are using the zebrafish adult pigment pattern . Previous work showed that ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetic",
"mutation",
"cell",
"differentiation",
"gene",
"function",
"developmental",
"biology",
"organism",
"development",
"stem",
"cells",
"molecular",
"development",
"morphogenesis",
"adult",
"stem",
"cells",
"stem",
"cell",
"niche",
"biology",
"regeneration",
"sign... | 2011 | Post-Embryonic Nerve-Associated Precursors to Adult Pigment Cells:
Genetic Requirements and Dynamics of Morphogenesis and
Differentiation |
The activity of neural populations in the brains of humans and animals can exhibit vastly different spatial patterns when faced with different tasks or environmental stimuli . The degrees of similarity between these neural activity patterns in response to different events are used to characterize the representational s... | We show the severity of the bias introduced when performing representational similarity analysis ( RSA ) based on neural activity pattern estimated within imaging runs . Our Bayesian RSA method significantly reduces the bias and can learn a shared representational structure across multiple participants . We also demons... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"learning",
"medicine",
"and",
"health",
"sciences",
"diagnostic",
"radiology",
"functional",
"magnetic",
"resonance",
"imaging",
"engineering",
"and",
"technology",
"signal",
"processing",
"social",
"sciences",
"random",
"variables",
"mathematical",
"models",
"neuroscien... | 2019 | Representational structure or task structure? Bias in neural representational similarity analysis and a Bayesian method for reducing bias |
Histone deacetylase Rpd3 is part of two distinct complexes: the large ( Rpd3L ) and small ( Rpd3S ) complexes . While Rpd3L targets specific promoters for gene repression , Rpd3S is recruited to ORFs to deacetylate histones in the wake of RNA polymerase II , to prevent cryptic initiation within genes . Methylation of h... | Acetylation of histone N-terminal tails occurs on nucleosomes as a gene is being transcribed , therefore helping the RNA polymerase II traveling through nucleosomes . Histone acetylation , however , has to be reversed in the wake of the polymerase in order to prevent transcription from initiating at the wrong place . R... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"molecular",
"biology/histone",
"modification",
"genetics",
"and",
"genomics/gene",
"expression",
"genetics",
"and",
"genomics/functional",
"genomics",
"genetics",
"and",
"genomics/chromosome",
"biology",
"molecular",
"biology/transcription",
"elongation",
"genetics",
"and",
... | 2010 | DSIF and RNA Polymerase II CTD Phosphorylation Coordinate the Recruitment of Rpd3S to Actively Transcribed Genes |
Working memory ( WM ) is the part of the brain's memory system that provides temporary storage and manipulation of information necessary for cognition . Although WM has limited capacity at any given time , it has vast memory content in the sense that it acts on the brain's nearly infinite repertoire of lifetime long-te... | Working memory ( WM ) is the part of the brain's vast memory system that provides temporary storage and manipulation of the information necessary for complex cognitive tasks , such as language comprehension , learning , and reasoning . Despite extensive neuroscience research , its mechanism is not clearly understood . ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"neuroscience/theoretical",
"neuroscience",
"computational",
"biology/computational",
"neuroscience"
] | 2010 | Spike-Timing Theory of Working Memory |
The opportunistic fungal pathogen Candida albicans frequently causes diseases such as oropharyngeal candidiasis ( OPC ) in immunocompromised individuals . Although it is well appreciated that the cytokine IL-17 is crucial for protective immunity against OPC , the cellular source and the regulation of this cytokine duri... | IL-17 is a key cytokine for immune homeostasis and host defense in barrier tissues , which can also drive inflammatory diseases and immunopathology under certain conditions . Most studies addressing IL-17-mediated processes focus on the lower gastrointestinal tract , while other barrier tissues such as the oral mucosa ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"blood",
"cells",
"flow",
"cytometry",
"innate",
"immune",
"system",
"medicine",
"and",
"health",
"sciences",
"immune",
"physiology",
"cytokines",
"pathology",
"and",
"laboratory",
"medicine",
"immune",
"cells",
"pathogens",
"immunology",
"microbiology",
"opportunistic"... | 2018 | Langerin+ DCs regulate innate IL-17 production in the oral mucosa during Candida albicans-mediated infection |
HTLV-I-specific CD8+ T cells have been characterized with high frequencies in peripheral blood and cerebrospinal fluid and production of proinflammatory cytokines , which contribute to central nervous system inflammation in HTLV-I-associated myelopathy/tropical spastic paraparesis ( HAM/TSP ) . However , little is know... | Human T-lymphotropic virus type I ( HTLV-I ) is a retrovirus that persistently infects 20 million people worldwide . The majority of infected individuals are asymptomatic carriers of the virus , but 5–10% of infected people develop either adult T cell leukemia/lymphoma ( ATL ) or a chronic , progressive neurological di... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"infectious",
"diseases/infectious",
"diseases",
"of",
"the",
"nervous",
"system",
"immunology/immunity",
"to",
"infections",
"infectious",
"diseases/viral",
"infections",
"immunology/leukocyte",
"activation"
] | 2009 | High Expression of CD244 and SAP Regulated CD8+ T Cell Responses of Patients with HTLV-I Associated Neurologic Disease |
While most yeast enzymes for the biosynthesis of glycerophospholipids , sphingolipids and ergosterol are known , genes for several postulated transporters allowing the flopping of biosynthetic intermediates and newly made lipids from the cytosolic to the lumenal side of the membrane are still not identified . An E-MAP ... | All living cells define their boundaries by lipid-containing membranes , which are impermeable to ions and water-soluble metabolic intermediates , and thus allow maintaining constant conditions inside the cells and stopping metabolic intermediates from diffusing away . Membranes are formed by amphiphilic lipids that ha... | [
"Abstract",
"Introduction",
"Results",
"and",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"sphingolipids",
"membrane",
"proteins",
"planar",
"chromatography",
"genetic",
"interactions",
"cellular",
"structures",
"and",
"organelles",
"thin-layer",
"chromatography",
"research",
"and",
"analysis",
"methods",
"lipids",
"chromosome",
"biology",
"cell",
"membranes",
... | 2016 | Chemogenetic E-MAP in Saccharomyces cerevisiae for Identification of Membrane Transporters Operating Lipid Flip Flop |
Model-based epidemiological assessment is useful to support decision-making at the beginning of an emerging Aedes-transmitted outbreak . However , early forecasts are generally unreliable as little information is available in the first few incidence data points . Here , we show how past Aedes-transmitted epidemics help... | In December , 2015 , Aedes mosquito-transmitted Zika outbreaks started in the French West Indies , about two years after chikungunya epidemics , spread by the same mosquito , hit the same region . Building on the similarities between these epidemics—regarding the route of transmission , the surveillance system , the po... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"geomorphology",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"togaviruses",
"chikungunya",
"infection",
"landforms",
"infectious",
"disease",
"epidemiology",
"pathogens",
"topography",
"tropical",
"diseases",
"microbiology",
"geogr... | 2018 | Improving early epidemiological assessment of emerging Aedes-transmitted epidemics using historical data |
The skin provides an important first line of defence and immunological barrier to invasive pathogens , but immune responses must also be regulated to maintain barrier function and ensure tolerance of skin surface commensal organisms . In schistosomiasis-endemic regions , populations can experience repeated percutaneous... | The skin is a major barrier protecting the host from pathogen infection , but is also a site for immune regulation . Using a murine model of repeated percutaneous exposure to infectious Schistosoma mansoni cercariae , we show that , in the skin , CD4+ T cells that do not express markers of conventional regulatory T cel... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Helminth Infection and Commensal Microbiota Drive Early IL-10 Production in the Skin by CD4+ T Cells That Are Functionally Suppressive |
Mammalian BET proteins comprise a family of bromodomain-containing epigenetic regulators with complex functions in chromatin organization and gene regulation . We identified the sole member of the BET protein family in Drosophila , Fs ( 1 ) h , as an inhibitor of the stress responsive transcription factor CncC , the fl... | Nrf2-related transcription factors regulate gene expression programs that protect organisms against chemical or oxidative stress . Nrf2-activating drugs hold promise for the treatment of diseases that are connected to oxidative stress or inflammation . We identified Fs ( 1 ) h , a bromodomain-containing BET protein , a... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"rna",
"interference",
"oxidative",
"stress",
"gene",
"regulation",
"regulatory",
"proteins",
"dna-binding",
"proteins",
"animals",
"animal",
"models",
"drosophila",
"melanogaster",
"model",
"organisms",
"pharmaceu... | 2016 | Keap1-Independent Regulation of Nrf2 Activity by Protein Acetylation and a BET Bromodomain Protein |
Human tuberculosis caused by M . bovis is a zoonosis presently considered sporadic in developed countries , but remains a poorly studied problem in low and middle resource countries . The disease in humans is mainly attributed to unpasteurized dairy products consumption . However , transmission due to exposure of human... | Mycobacterium tuberculosis complex causes tuberculosis in humans and other mammals . The complex includes M . bovis , which causes bovine tuberculosis . The main route of transmission of this zoonosis is the consumption of unpasteurized dairy products . Nevertheless , exposure to infected cattle while performing husban... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases",
"bovine",
"tuberculosis",
"in",
"humans",
"neglected",
"tropical",
"diseases"
] | 2013 | Prevalence of Latent and Active Tuberculosis among Dairy Farm Workers Exposed to Cattle Infected by Mycobacterium bovis |
Post-synaptic potential ( PSP ) variability is typically attributed to mechanisms inside synapses , yet recent advances in experimental methods and biophysical understanding have led us to reconsider the role of axons as highly reliable transmission channels . We show that in many thin axons of our brain , the action p... | The fundamental signal of the nervous system is the action potential: an electrical spike propagated along neurons and transmitted between them via synapses . Once triggered , action potentials are generally assumed to be robust to noise , and the variability observed at all levels of the nervous system is primarily at... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"computational",
"neuroscience",
"neuroscience",
"biology",
"and",
"life",
"sciences",
"computational",
"biology"
] | 2014 | Axonal Noise as a Source of Synaptic Variability |
Phleboviruses transmitted by sandflies are endemic in the Mediterranean area . The last decade has witnessed the description of an accumulating number of novel viruses . Although , the risk of exposure of vertebrates is globally assessed , detailed geographic knowledge is poor even in Greece and Cyprus where sandfly fe... | Phleboviruses transmitted by sandflies are endemic in the Mediterranean basin . An increased number of new viruses was described during the last decade . However , levels of exposure of human and animal populations are poorly known . A total of 1 , 250 dogs from Greece and 422 dogs from Cyprus were tested for the prese... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"animal",
"types",
"greece",
"medicine",
"and",
"health",
"sciences",
"immune",
"physiology",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"immunology",
"geographical",
"locations",
"microbiology",
"vertebrates",
"sand",
"flies",
"pets",
"and",
"companion"... | 2016 | Seroprevalence of Sandfly‐Borne Phleboviruses Belonging to Three Serocomplexes (Sandfly fever Naples, Sandfly fever Sicilian and Salehabad) in Dogs from Greece and Cyprus Using Neutralization Test |
Rabies is a neglected zoonotic disease . Given the low incidence , apart from the existing reporting syst , there is a need to look for other means of case detection strategies for rabies . Contact tracing is one such method to efficiently capture information . To find out the rabid status of biting animal through cont... | In India , Rabies is a neglected zoonotic disease and the burden of rabies is usually not captured by the health system due to varied reasons . Hence , an exploratory study was attempted to find out the rabid status of the biting animal through contact tracing during the first quarter of 2017 in villages coming under t... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"post-exposure",
"prophylaxis",
"tropical",
"diseases",
"microbiology",
"vertebrates",
"dogs",
"animals",
"mammals",
"health",
"care",
"viruses",
"preventive",
"medicine",
... | 2018 | An exploratory study on rabies exposure through contact tracing in a rural area near Bengaluru, Karnataka, India |
A review of 400 clinical records of paracoccidioidomycosis ( PCM ) patients , 93 with the acute/subacute ( AF ) and 307 with the chronic form ( CF ) , attended from 1977 to 2011 , selected as to the schedule of release for study by the Office of Medical Records at the University Hospital of the Faculdade de Medicina de... | Paracoccidioidomycosis ( PCM ) is a systemic mycosis caused by fungi of the Paracoccidioides brasiliensis and Paracoccidioides lutzii complexes , which live in the soil and affect mainly rural workers in the most productive period of their lives . PCM can relapse after effective treatment because quiescent fungi can re... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases",
"medicine",
"and",
"health",
"sciences",
"diagnostic",
"medicine",
"clinical",
"immunology",
"biology",
"and",
"life",
"sciences",
"immunology"
] | 2014 | Prevalence and Serological Diagnosis of Relapse in Paracoccidioidomycosis Patients |
Candida is the most common human fungal pathogen and causes systemic infections that require neutrophils for effective host defense . Humans deficient in the C-type lectin pathway adaptor protein CARD9 develop spontaneous fungal disease that targets the central nervous system ( CNS ) . However , how CARD9 promotes prot... | CARD9 is a molecule expressed by mammalian immune cells and is centrally positioned downstream of several C-type lectin receptors , which sense fungi . The critical role of CARD9 in the activation of antifungal host defense has been highlighted by the demonstration that human mutations that disrupt the function of CARD... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2015 | CARD9-Dependent Neutrophil Recruitment Protects against Fungal Invasion of the Central Nervous System |
Recent studies have suggested that the thermodynamic stability of mRNA secondary structure near the start codon can regulate translation efficiency in Escherichia coli , and that translation is more efficient the less stable the secondary structure . We survey the complete genomes of 340 species for signals of reduced ... | Synonymous mutations are mutations that change the nucleotide sequence of a gene without changing the amino-acid sequence . Because these mutations don't alter the expressed protein , they are frequently also called silent mutations . Yet increasing evidence demonstrates that synonymous mutations are not that silent . ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"molecular",
"biology/molecular",
"evolution",
"molecular",
"biology/translational",
"regulation",
"genetics",
"and",
"genomics/bioinformatics",
"evolutionary",
"biology/genomics"
] | 2010 | A Universal Trend of Reduced mRNA Stability near the Translation-Initiation Site in Prokaryotes and Eukaryotes |
The segmentation gene network in Drosophila embryo solves the fundamental problem of embryonic patterning: how to establish a periodic pattern of gene expression , which determines both the positions and the identities of body segments . The gap gene network constitutes the first zygotic regulatory tier in this process... | Systems biology is aimed to develop an understanding of biological function or process as a system of interacting components . Here we apply the systems-level approach to understand how the blueprints for segments in the fruit fly Drosophila embryo arise . We obtain gene expression data and use the gene circuits method... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"systems",
"biology",
"developmental",
"biology",
"gene",
"regulation",
"gene",
"expression",
"regulatory",
"networks",
"molecular",
"genetics",
"biology",
"computational",
"biology",
"genetics",
"gene",
"networks",
"pattern",
"formation",
"genetics",
"and",
"genomics"
] | 2012 | Modeling of Gap Gene Expression in Drosophila Kruppel Mutants |
Every year , influenza epidemics affect millions of people and place a strong burden on health care services . A timely knowledge of the onset of the epidemic could allow these services to prepare for the peak . We present a method that can reliably identify and signal the influenza outbreak . By combining official Inf... | Influenza , generally referred to as the flu , is a common infectious disease that affects millions of people . Every year , we expect this seasonal disease to occur during the Winter , but exactly when it will start and how severe it will be is not known . This places a strong burden on health services , as often the ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"influenza",
"applied",
"mathematics",
"geographical",
"locations",
"epidemiological",
"methods",
"and",
"statistics",
"simulation",
"and",
"modeling",
"algorithms",
"seasons",
"mathematics",
"infectious",
"disease",
"control",
"re... | 2017 | Early and Real-Time Detection of Seasonal Influenza Onset |
Although hypoxia is a major stress on physiological processes , several human populations have survived for millennia at high altitudes , suggesting that they have adapted to hypoxic conditions . This hypothesis was recently corroborated by studies of Tibetan highlanders , which showed that polymorphisms in candidate g... | Although hypoxia is a major stress on physiological processes , several human populations have survived for millennia at high altitudes , suggesting that they have adapted to hypoxic conditions . Consistent with this idea , previous studies have identified genetic variants in Tibetan highlanders associated with reducti... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genome-wide",
"association",
"studies",
"medicine",
"population",
"genetics",
"global",
"health",
"epigenetics",
"biology",
"evolutionary",
"genetics",
"adaptation",
"natural",
"selection",
"genetics",
"genomics",
"evolutionary",
"biology",
"genomic",
"evolution",
"evoluti... | 2012 | The Genetic Architecture of Adaptations to High Altitude in Ethiopia |
Miltefosine ( MIL ) is an oral antileishmanial drug used for treatment of visceral leishmaniasis ( VL ) in the Indian subcontinent . Recent reports indicate a significant decline in its efficacy with a high rate of relapse in VL as well as post kala-azar dermal leishmaniasis ( PKDL ) . We investigated the parasitic fac... | Increasing rate of relapse against miltefosine ( MIL ) and decline in its efficacy prompted us to study the parasitic factors associated with MIL unresponsiveness in clinical isolates of Leishmania donovani . Studies to explore the mechanism of MIL resistance in L . donovani are largely restricted to experimentally ind... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"chemical",
"compounds",
"oxidative",
"stress",
"immunology",
"tropical",
"diseases",
"microbiology",
"parasitic",
"diseases",
"parasitic",
"protozoans",
"protozoan",
"life",
"cycles",
"organi... | 2017 | Increased miltefosine tolerance in clinical isolates of Leishmania donovani is associated with reduced drug accumulation, increased infectivity and resistance to oxidative stress |
Epilepsy and progressively worsening severe chronic headaches ( WSCH ) are the two most common clinical manifestations of neurocysticercosis , a form of cysticercosis . Most community-based studies in sub-Saharan Africa ( SSA ) use a two-step approach ( questionnaire and confirmation ) to estimate the prevalence of the... | Epilepsy and progressively worsening severe chronic headaches are the two most common clinical manifestations of neurocysticercosis , a form of cysticercosis . To understand where the prevalence of these neurological disorders is highest for targeted infection control , valid prevalence estimates are needed . Most neur... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"physicians",
"medical",
"doctors",
"pathology",
"and",
"laboratory",
"medicine",
"neurocysticercosis",
"medical",
"personnel",
"tropical",
"diseases",
"parasitic",
"diseases",
"migraine",
"health",
"care",
"headaches",
"research",... | 2019 | The impact of imperfect screening tools on measuring the prevalence of epilepsy and headaches in Burkina Faso |
DNA sequences capable of adopting non-canonical secondary structures have been associated with gross-chromosomal rearrangements in humans and model organisms . Previously , we have shown that long inverted repeats that form hairpin and cruciform structures and triplex-forming GAA/TTC repeats induce the formation of dou... | Eukaryotic chromosomes include regions that are susceptible for breakage and rearrangements . Repeats that can adopt non-B form DNA secondary structure are often found to be responsible for the induction of rearrangements . Here , we demonstrate that inverted repeats and GAA/TTC breakage sites are also sources of point... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"gene",
"identification",
"and",
"analysis",
"genetics",
"molecular",
"genetics",
"biology"
] | 2013 | Fragile DNA Motifs Trigger Mutagenesis at Distant Chromosomal Loci in Saccharomyces cerevisiae |
Urinary tract infection ( UTI ) is one of the most common bacterial infections with frequent recurrence being a major medical challenge . Development of effective therapies has been impeded by the lack of knowledge of events leading to adaptive immunity . Here , we establish conclusive evidence that an adaptive immune ... | Urinary tract infection is a common infection with a high propensity for recurrence . The majority of infections are caused by uropathogenic E . coli , a growing public health concern with increasing prevalence of antibiotic resistant strains . Finding therapeutic options that circumvent the need for antibiotics , whil... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Macrophages Subvert Adaptive Immunity to Urinary Tract Infection |
The continuously prolonged human lifespan is accompanied by increase in neurodegenerative diseases incidence , calling for the development of inexpensive blood-based diagnostics . Analyzing blood cell transcripts by RNA-Seq is a robust means to identify novel biomarkers that rapidly becomes a commonplace . However , th... | Long non-coding RNAs ( lncRNAs ) comprise a novel , fascinating class of RNAs with largely unknown biological functions . Parkinson's-disease ( PD ) is the most frequent motor disorder , and Deep-brain-stimulation ( DBS ) treatment alleviates the symptoms , but early disease biomarkers are still unknown and new future ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genome",
"sequencing",
"genome",
"expression",
"analysis",
"neurobiology",
"of",
"disease",
"and",
"regeneration",
"genome",
"analysis",
"tools",
"functional",
"genomics",
"gene",
"expression",
"biology",
"genomics",
"molecular",
"cell",
"biology",
"neuroscience",
"tra... | 2014 | Long Non-Coding RNA and Alternative Splicing Modulations in Parkinson's Leukocytes Identified by RNA Sequencing |
In vertebrate embryos , the earliest definitive marker for the neural plate , which will give rise to the entire central nervous system , is the transcription factor Sox2 . Although some of the extracellular signals that regulate neural plate fate have been identified , we know very little about the mechanisms controll... | During early development , when the embryo has three layers of cells ( ectoderm , mesoderm , and endoderm ) , a region of the ectoderm called the neural plate becomes specified to generate the entire nervous system . One of the earliest molecular markers for the neural plate is the transcription factor Sox2 , which is ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods",
"Supporting",
"Information"
] | [
"developmental",
"biology",
"cell",
"biology",
"neuroscience",
"molecular",
"biology"
] | 2008 | A Mechanism Regulating the Onset of Sox2 Expression in the Embryonic Neural Plate |
Various characteristics of complex gene regulatory networks ( GRNs ) have been discovered during the last decade , e . g . , redundancy , exponential indegree distributions , scale-free outdegree distributions , mutational robustness , and evolvability . Although progress has been made in this field , it is not well un... | Various organismal traits , including the morphology of multicellular species and metabolism in unicellular species , are determined by the amount and combinations of proteins in the cell . The complex regulatory network plays an important role in controlling the protein profiles in a cell . Recent studies have reveale... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"evolutionary",
"biology/microbial",
"evolution",
"and",
"genomics",
"computational",
"biology/transcriptional",
"regulation",
"genetics",
"and",
"genomics/gene",
"expression",
"evolutionary",
"biology/genomics",
"computational",
"biology/evolutionary",
"modeling",
"developmental",... | 2010 | Evolution of Gene Regulatory Networks by Fluctuating Selection and Intrinsic Constraints |
Bacteria use a variety of secreted virulence factors to manipulate host cells , thereby causing significant morbidity and mortality . We report a mechanism for the long-distance delivery of multiple bacterial virulence factors , simultaneously and directly into the host cell cytoplasm , thus obviating the need for dire... | Gram-negative pathogens are responsible for 2 million annual hospital-acquired infections , adding tremendously to U . S . healthcare costs . Pseudomonas aeruginosa , an opportunistic human pathogen , is commonly associated with nosocomial infections , particularly ventilator-associated infections and pseudomonal pneum... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"infectious",
"diseases/nosocomial",
"and",
"healthcare-associated",
"infections",
"respiratory",
"medicine/respiratory",
"infections",
"cell",
"biology/membranes",
"and",
"sorting",
"infectious",
"diseases/bacterial",
"infections",
"cell",
"biology/cytoskeleton"
] | 2009 | Long-Distance Delivery of Bacterial Virulence Factors by Pseudomonas aeruginosa Outer Membrane Vesicles |
Traditional genetic association studies are very difficult in bacteria , as the generally limited recombination leads to large linked haplotype blocks , confounding the identification of causative variants . Beta-lactam antibiotic resistance in Streptococcus pneumoniae arises readily as the bacteria can quickly incorpo... | Streptococcus pneumoniae is carried asymptomatically in the nasopharyngeal tract . However , it is capable of causing multiple diseases , including pneumonia , bacteraemia and meningitis , which are common causes of morbidity and mortality in young children . Antibiotic treatment has become more difficult , especially ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"biology",
"and",
"life",
"sciences",
"population",
"biology",
"microbiology"
] | 2014 | Comprehensive Identification of Single Nucleotide Polymorphisms Associated with Beta-lactam Resistance within Pneumococcal Mosaic Genes |
Genome rearrangements often result from non-allelic homologous recombination ( NAHR ) between repetitive DNA elements dispersed throughout the genome . Here we systematically analyze NAHR between Ty retrotransposons using a genome-wide approach that exploits unique features of Saccharomyces cerevisiae purebred and Sacc... | The human genome is structurally dynamic , frequently undergoing loss , duplication , and rearrangement of large chromosome segments . These structural changes occur both in normal and in cancerous cells and are thought to cause both benign and deleterious changes in cell function . Many of these structural alterations... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"molecular",
"biology/recombination",
"molecular",
"biology/chromosome",
"structure",
"molecular",
"biology/dna",
"repair"
] | 2010 | Competitive Repair by Naturally Dispersed Repetitive DNA during Non-Allelic Homologous Recombination |
Synaptic communication is a dynamic process that is key to the regulation of neuronal excitability and information processing in the brain . To date , however , the molecular signals controlling synaptic dynamics have been poorly understood . Membrane-derived bioactive phospholipids are potential candidates to control ... | Neuronal networks are modules of synaptic connectivity that underlie all brain functions , from simple reflexes to complex cognitive processes . Synaptic plasticity allows these networks to adapt to changing external and internal environments . Membrane-derived bioactive phospholipids are potential candidates to contro... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Membrane-Derived Phospholipids Control Synaptic Neurotransmission and Plasticity |
cis-Regulatory DNA elements contain multiple binding sites for activators and repressors of transcription . Among these elements are enhancers , which establish gene expression states , and Polycomb/Trithorax response elements ( PREs ) , which take over from enhancers and maintain transcription states of several hundre... | The evolution of regulatory DNA plays a crucial role in making species different from one another . One way to study the evolution of regulatory DNA is by genome alignment , which assumes that elements with conserved function will be found in conserved pieces of DNA . Although conservation does imply function , it does... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"developmental",
"biology",
"computational",
"biology",
"evolutionary",
"biology",
"genetics",
"and",
"genomics"
] | 2008 | Evolutionary Plasticity of Polycomb/Trithorax Response Elements in Drosophila Species |
Trypanosoma cruzi has three distinct life cycle stages; epimastigote , trypomastigote , and amastigote . Amastigote is the replication stage in host mammalian cells , hence this stage of parasite has clinical significance in drug development research . Presence of extracellular amastigotes ( EA ) and their infection ca... | We developed an experimental system to study amastigote stage of Trypanosoma cruzi as a proliferable axenic culture . Use of axenic amastigotes allows us to directly introduce exogenous gene into T . cruzi amastigote and select for drug resistant parasite to enrich the transfectants . Our strategy bypasses differentiat... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"transfection",
"viral",
"transmission",
"and",
"infection",
"microbiology",
"parasitic",
"protozoans",
"protozoan",
"life",
"cycles",
"developmental",
"biology",
"trypomastigotes",
"protozoans",
"molecular",
"biology",
"techniques",
"epimastigotes",
"research",
"and",
"ana... | 2019 | Utilization of proliferable extracellular amastigotes for transient gene expression, drug sensitivity assay, and CRISPR/Cas9-mediated gene knockout in Trypanosoma cruzi |
Linked to extreme rates of chronic heart and kidney disease , pyoderma is endemic amongst Aboriginal children in Australia's Northern Territory ( NT ) . Many of those with pyoderma will also have scabies . We report the results of a community-based collaboration within the East Arnhem Region , which aimed to reduce the... | Skin infections are endemic in many in remote Australian Aboriginal communities and have been linked to very high rates of chronic heart and kidney disease in this population . We report the results of a regional collaboration that aimed to reduce skin infections amongst children aged less than 15 years in five remote ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"dermatology/pediatric",
"skin",
"diseases,",
"including",
"genetic",
"diseases",
"infectious",
"diseases/neglected",
"tropical",
"diseases",
"dermatology/skin",
"infections",
"public",
"health",
"and",
"epidemiology/infectious",
"diseases",
"infectious",
"diseases/skin",
"infe... | 2009 | A Regional Initiative to Reduce Skin Infections amongst Aboriginal Children Living in Remote Communities of the Northern Territory, Australia |
Parasitic protozoa such as the apicomplexan Toxoplasma gondii progress through their life cycle in response to stimuli in the environment or host organism . Very little is known about how proliferating tachyzoites reprogram their expressed genome in response to stresses that prompt development into latent bradyzoite cy... | Protozoan parasites cause significant disease in humans and livestock , and many of our current therapies have serious side effects or are being rendered useless due to the development of drug resistance . These parasites typically have complex life cycles involving multiple hosts and some , like Toxoplasma gondii , ha... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/epigenetics",
"molecular",
"biology/chromatin",
"structure",
"microbiology/parasitology"
] | 2010 | Toxoplasma gondii Lysine Acetyltransferase GCN5-A Functions in the Cellular Response to Alkaline Stress and Expression of Cyst Genes |
Campylobacter jejuni is a major food-borne pathogen and a common causative agent of human enterocolitis . Fluoroquinolones are a key class of antibiotics prescribed for clinical treatment of enteric infections including campylobacteriosis , but fluoroquinolone-resistant Campylobacter readily emerges under the antibioti... | As a food-borne bacterial pathogen , Campylobacter jejuni is a common causative agent of gastrointestinal illnesses in humans . Development of antibiotic resistance in Campylobacter , especially to fluoroquinolone ( a broad-spectrum antimicrobial ) , compromises clinical treatments and presents a major public health th... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"infectious",
"diseases/bacterial",
"infections",
"infectious",
"diseases/gastrointestinal",
"infections",
"infectious",
"diseases/antimicrobials",
"and",
"drug",
"resistance",
"microbiology"
] | 2008 | Key Role of Mfd in the Development of Fluoroquinolone Resistance in Campylobacter jejuni |
A proportion of all immunocompetent patients treated for visceral leishmaniasis ( VL ) are known to relapse; however , the risk factors for relapse are not well understood . With the support of the Rajendra Memorial Research Institute ( RMRI ) , Médecins Sans Frontières ( MSF ) implemented a program in Bihar , India , ... | Visceral leishmaniasis ( VL ) , also known as Kala azar , accounts for the second-highest burden of parasitic disease worldwide . Fifty percent of VL cases worldwide occur in India , and up to 90% of these in the state of Bihar . Up to 10% of VL patients relapse within 6 months of treatment , particularly if co-infecte... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2014 | Risk Factors for Visceral Leishmaniasis Relapse in Immunocompetent Patients following Treatment with 20 mg/kg Liposomal Amphotericin B (Ambisome) in Bihar, India |
5-Aza-2′-deoxycytidine , approved by the FDA for the treatment of myelodysplastic syndrome ( MDS ) , is incorporated into the DNA of dividing cells where it specifically inhibits DNA methylation by forming covalent complexes with the DNA methyltransferases ( DNMTs ) . In an effort to study the correlations between DNA ... | Epigenetic changes , which include chemical modifications to the DNA and changes in the proteins that package DNA to fit into a cell , play an important role in gene expression regulation . The fact that a number of abnormal epigenetic changes that lead to the silencing of genes occur during tumorigenesis has prompted ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"oncology",
"medicine",
"gene",
"expression",
"genetics",
"cancer",
"treatment",
"biology",
"genetics",
"and",
"genomics"
] | 2012 | Gene Reactivation by 5-Aza-2′-Deoxycytidine–Induced Demethylation Requires SRCAP–Mediated H2A.Z Insertion to Establish Nucleosome Depleted Regions |
Fascioliasis is an emerging zoonotic disease of considerable veterinary and public health importance . Triclabendazole is the only available drug for treatment . Laboratory studies have documented promising fasciocidal properties of the artemisinins ( e . g . , artemether ) . We carried out two exploratory phase-2 tria... | Fasciola hepatica and F . gigantica are two liver flukes that parasitize herbivorous large size mammals ( e . g . , sheep and cattle ) , as well as humans . A single drug is available to treat infections with Fasciola flukes , namely , triclabendazole . Recently , laboratory studies and clinical trials in sheep and hum... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases",
"drugs",
"and",
"devices",
"neglected",
"tropical",
"diseases",
"veterinary",
"science",
"veterinary",
"medicine"
] | 2011 | Efficacy and Safety of Artemether in the Treatment of Chronic Fascioliasis in Egypt: Exploratory Phase-2 Trials |
The synaptonemal complex ( SC ) is a proteinaceous , meiosis-specific structure that is highly conserved in evolution . During meiosis , the SC mediates synapsis of homologous chromosomes . It is essential for proper recombination and segregation of homologous chromosomes , and therefore for genome haploidization . Mut... | Meiosis is a special type of cell division that takes place in the germ line of sexually reproducing diploid organisms . Major events during meiosis are the pairing , recombination , and segregation of homologous chromosomes . As a consequence , daughter cells are haploid and genetically diverse . Therefore , meiosis i... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"meiosis",
"chromosome",
"biology",
"biology",
"genomics",
"genetics",
"and",
"genomics"
] | 2011 | A Novel Mouse Synaptonemal Complex Protein Is Essential for Loading of Central Element Proteins, Recombination, and Fertility |
Tropical coral reefs feature extraordinary biodiversity and high productivity rates in oligotrophic waters . Due to increasing frequencies of perturbations – anthropogenic and natural – many reefs are under threat . Such perturbations often have devastating effects on these unique ecosystems and especially if they occu... | The degradation of coral reefs is a major threat for tropical coastal environments , worldwide . For this reason we developed a spatially explicit model which simulates competition in a benthic reef community under the influence of various environmental factors . Here we highlight the impact of two major perturbation t... | [
"Abstract",
"Introduction",
"Results",
"Discussion"
] | [
"simulation",
"languages",
"community",
"structure",
"computerized",
"simulations",
"marine",
"biology",
"corals",
"coral",
"reefs",
"marine",
"and",
"aquatic",
"sciences",
"biology",
"community",
"ecology",
"computer",
"science",
"programming",
"languages",
"ecology",
... | 2012 | Simulations of Long-Term Community Dynamics in Coral Reefs - How Perturbations Shape Trajectories |
Genome-wide association studies are revolutionizing the search for the genes underlying human complex diseases . The main decisions to be made at the design stage of these studies are the choice of the commercial genotyping chip to be used and the numbers of case and control samples to be genotyped . The most common me... | Genome-wide association studies are a powerful and now widely-used method for finding genetic variants that increase the risk of developing particular diseases . These studies are complex and must be planned carefully in order to maximize the probability of finding novel associations . The main design choices to be mad... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"genetics",
"and",
"genomics/disease",
"models",
"genetics",
"and",
"genomics/complex",
"traits",
"genetics",
"and",
"genomics/bioinformatics",
"genetics",
"and",
"genomics/population",
"genetics"
] | 2009 | Designing Genome-Wide Association Studies: Sample Size, Power, Imputation, and the Choice of Genotyping Chip |
Anti-tumor necrosis factor alpha ( anti-TNF ) biologic therapy is a widely used treatment for rheumatoid arthritis ( RA ) . It is unknown why some RA patients fail to respond adequately to anti-TNF therapy , which limits the development of clinical biomarkers to predict response or new drugs to target refractory cases ... | There are no genetic predictors of response to one of the most widely used classes of drugs in the treatment of rheumatoid arthritis—biological modifiers of the inflammatory cytokine tumor necrosis factor-alpha ( or anti-TNF therapy ) . To identify genetic predictors , we performed the largest genome-wide association s... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"genome-wide",
"association",
"studies",
"gene",
"expression",
"genetics",
"biology",
"genetics",
"and",
"genomics"
] | 2013 | Genome-Wide Association Study and Gene Expression Analysis Identifies CD84 as a Predictor of Response to Etanercept Therapy in Rheumatoid Arthritis |
Meiotic mapping of quantitative trait loci regulating expression ( eQTLs ) has allowed the construction of gene networks . However , the limited mapping resolution of these studies has meant that genotype data are largely ignored , leading to undirected networks that fail to capture regulatory hierarchies . Here we use... | An important problem in systems biology is to map gene networks , which help identify gene functions and discover critical disease pathways . Current methods for constructing gene networks have identified a number of biologically significant functional modules . However , these networks do not reveal directionality , t... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"genetics",
"and",
"genomics/genomics",
"genetics",
"and",
"genomics/animal",
"genetics",
"computational",
"biology/systems",
"biology",
"computational",
"biology/transcriptional",
"regulation",
"genetics",
"and",
"genomics/gene",
"expression",
"molecular",
"biology/bioinformatic... | 2009 | Directed Mammalian Gene Regulatory Networks Using Expression and Comparative Genomic Hybridization Microarray Data from Radiation Hybrids |
Direct-acting antiviral agents ( DAAs ) for hepatitis C treatment tend to fare better in individuals who are also likely to respond well to interferon-alpha ( IFN ) , a surprising correlation given that DAAs target specific viral proteins whereas IFN triggers a generic antiviral immune response . Here , we posit a caus... | Treatment of hepatitis C virus ( HCV ) infection is seeing a paradigm shift with powerful drugs called direct-acting antiviral agents ( DAAs ) replacing earlier treatments involving interferon ( IFN ) . DAAs target specific HCV proteins . IFN stimulates our immune response against HCV . The two should thus work indepen... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"viral",
"transmission",
"and",
"infection",
"hepacivirus",
"pathogens",
"microbiology",
"viral",
"structure",
"liver",
"diseases",
"viruses",
"rna",
"viruses",
"pharmaceutics",
"gast... | 2018 | Modelling how responsiveness to interferon improves interferon-free treatment of hepatitis C virus infection |
Dendritic cells ( DCs ) as professional antigen-presenting cells play an important role in the initiation and modulation of the adaptive immune response . However , their role in the innate immune response against bacterial infections is not completely defined . Here we have analyzed the role of DCs and their impact on... | Dendritic cells ( DCs ) are professional antigen-presenting cells playing a crucial role in the initiation of T-cell responses to combat infection . DCs adapt their immune response according to the type of pathogen . For example , in response to intracellular bacteria , DCs produce IL-12 , thereby initiating Th1 polari... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"infectious",
"diseases",
"immune",
"cells",
"immunity",
"immunology",
"biology",
"microbiology",
"bacterial",
"pathogens",
"immune",
"system"
] | 2012 | Depletion of Dendritic Cells Enhances Innate Anti-Bacterial Host Defense through Modulation of Phagocyte Homeostasis |
Lentiviruses such as HIV-1 traverse nuclear pore complexes ( NPC ) and infect terminally differentiated non-dividing cells , but how they do this is unclear . The cytoplasmic NPC protein Nup358/RanBP2 was identified as an HIV-1 co-factor in previous studies . Here we report that HIV-1 capsid ( CA ) binds directly to th... | During infection HIV-1 enters the nucleus by crossing the nuclear membrane and incorporating itself into the host DNA by a process called integration . Here we show that the viral capsid protein gets tethered to a cyclophilin protein called Nup358 , a component of the nuclear membrane gateways that allow transport betw... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"biochemistry",
"infectious",
"diseases",
"molecular",
"cell",
"biology",
"immunology",
"biology",
"microbiology",
"evolutionary",
"biology",
"proteomics"
] | 2011 | HIV-1 Capsid-Cyclophilin Interactions Determine Nuclear Import Pathway, Integration Targeting and Replication Efficiency |
While the induction of broadly neutralizing antibodies ( bNAbs ) is a major goal of HIV vaccination strategies , there is mounting evidence to suggest that antibodies with Fc effector function also contribute to protection against HIV infection . Here we investigated Fc effector functionality of HIV-specific IgG plasma... | Some HIV-infected individuals develop antibodies that are capable of neutralizing the majority of HIV strains , a highly desirable function mediated by the antibody Fab portion . While antibodies elicited by current vaccines have failed to recreate this activity , the partial protection seen in the RV144 vaccine trial ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"blood",
"cells",
"hiv",
"infections",
"medicine",
"and",
"health",
"sciences",
"immune",
"physiology",
"immune",
"cells",
"pathology",
"and",
"laboratory",
"medicine",
"viral",
"transmission",
"and",
"infection",
"pathogens",
"immunology",
"cell",
"processes",
"micro... | 2018 | HIV-specific Fc effector function early in infection predicts the development of broadly neutralizing antibodies |
Identifying a protein's functional sites is an important step towards characterizing its molecular function . Numerous structure- and sequence-based methods have been developed for this problem . Here we introduce ConCavity , a small molecule binding site prediction algorithm that integrates evolutionary sequence conse... | Protein molecules are ubiquitous in the cell; they perform thousands of functions crucial for life . Proteins accomplish nearly all of these functions by interacting with other molecules . These interactions are mediated by specific amino acid positions in the proteins . Knowledge of these “functional sites” is crucial... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"computational",
"biology/macromolecular",
"structure",
"analysis",
"computer",
"science",
"molecular",
"biology/bioinformatics",
"computational",
"biology/macromolecular",
"sequence",
"analysis",
"computational",
"biology"
] | 2009 | Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure |
Over the last 15 years , visceral leishmaniasis ( VL ) has emerged as a public health concern in Tbilisi , the capital of Georgia . Seroepidemiological surveys were conducted to determine the prevalence and incidence of infection in children and dogs within the main focus of VL , and to identify risk factors associated... | Visceral leishmaniasis ( VL ) has emerged as a public health problem in Tbilisi , the capital of Georgia . Dogs are the main infection reservoirs for transmission by sand flies of Leishmania infantum to humans , many of whom may become infected without developing disease . Since majority of cases are in children we wer... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases",
"public",
"health",
"and",
"epidemiology",
"epidemiology",
"infectious",
"disease",
"epidemiology",
"leishmaniasis",
"neglected",
"tropical",
"diseases",
"infectious",
"disease",
"control"
] | 2011 | Epidemiologic Aspects of an Emerging Focus of Visceral Leishmaniasis in Tbilisi, Georgia |
Epstein-Barr virus ( EBV ) is a ubiquitous human γ-herpesvirus that can give rise to cancers of both B-cell and epithelial cell origin . In EBV-induced cancers of epithelial origin , including nasopharyngeal carcinomas ( NPCs ) and gastric carcinomas , the latent EBV genome expresses very high levels of a cluster of 22... | One important innate immune response to viral infection is apoptosis , also called programmed cell death , whereby the infected cells commit suicide rather than serve as factories for virus production . As a result , many viruses have developed strategies to inhibit apoptosis . Here , we demonstrate that five of the Ep... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | EBV BART MicroRNAs Target Multiple Pro-apoptotic Cellular Genes to Promote Epithelial Cell Survival |
The latent EBV nuclear antigen 3C ( EBNA3C ) is required for transformation of primary human B lymphocytes . Most mature B-cell malignancies originate from malignant transformation of germinal center ( GC ) B-cells . The GC reaction appears to have a role in malignant transformation , in which a major player of the GC ... | Epstein-Barr virus ( EBV ) is the first characterized human tumor virus , which is associated with a broad range of human cancers . One of the latent proteins , EBV encoded nuclear antigen 3C ( EBNA3C ) plays a critical role in EBV-mediated B-cell transformation . Bcl6 is a master regulator required in mature B-cells d... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immunology",
"messenger",
"rna",
"cancers",
"and",
"neoplasms",
"cell",
"processes",
"rna",
"extraction",
"dna-binding",
"proteins",
"oncology",
"hematologic",
"cancers",
"and",
"related",
... | 2017 | An essential EBV latent antigen 3C binds Bcl6 for targeted degradation and cell proliferation |
The advent of high-throughput sequencing techniques has made it possible to follow the genomic evolution of pathogenic bacteria by comparing longitudinally collected bacteria sampled from human hosts . Such studies in the context of chronic airway infections by Pseudomonas aeruginosa in cystic fibrosis ( CF ) patients ... | Patients with cystic fibrosis ( CF ) are often colonized by a single clone of the common , widespread bacterium Pseudomonas aeruginosa , resulting in chronic airway infections . Long-term persistence of the bacteria involves the emergence and selection of multiple phenotypic variants . Among these are “mutator” variant... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"bacterial",
"genomics",
"organismal",
"evolution",
"microbial",
"mutation",
"microbial",
"evolution",
"genetics",
"biology",
"and",
"life",
"sciences",
"microbiology",
"genomics",
"evolutionary",
"biology",
"bacterial",
"evolution",
"microbial",
"genomics"
] | 2014 | Coexistence and Within-Host Evolution of Diversified Lineages of Hypermutable Pseudomonas aeruginosa in Long-term Cystic Fibrosis Infections |
The relative roles of the endosomal TLR3/7/8 versus the intracellular RNA helicases RIG-I and MDA5 in viral infection is much debated . We investigated the roles of each pattern recognition receptor in rhinovirus infection using primary bronchial epithelial cells . TLR3 was constitutively expressed; however , RIG-I and... | Host-pathogen interactions are mediated by pattern recognition receptors that identify conserved structures of micro-organisms that are distinct from self . During a viral infection , important pattern recognition receptors include the endosomal Toll-like receptors ( TLRs ) , and a second set of cytoplasmic pattern rec... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"immunology/cellular",
"microbiology",
"and",
"pathogenesis",
"immunology/innate",
"immunity",
"infectious",
"diseases/viral",
"infections",
"infectious",
"diseases/respiratory",
"infections",
"immunology/immunity",
"to",
"infections"
] | 2010 | Co-ordinated Role of TLR3, RIG-I and MDA5 in the Innate Response to Rhinovirus in Bronchial Epithelium |
Herpes simplex encephalitis ( HSE ) is a fatal infection of the central nervous system ( CNS ) predominantly caused by Herpes simplex virus type 1 . Factors regulating the susceptibility to HSE are still largely unknown . To identify host gene ( s ) regulating HSE susceptibility we performed a genome-wide linkage scan ... | Herpes simplex encephalitis ( HSE ) is a rare , but severe infection of the central nervous system ( CNS ) caused by Herpes simplex virus type 1 . We have previously characterized a model for HSE in the inbred DA rat which resembles human HSE . Interestingly the inbred PVG rat is completely resistant to the disease and... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"infectious",
"diseases",
"infectious",
"diseases",
"of",
"the",
"nervous",
"system",
"herpes",
"simplex",
"neurology",
"neurological",
"disorders",
"viral",
"diseases",
"encephalitis"
] | 2012 | The Calcitonin Receptor Gene Is a Candidate for Regulation of Susceptibility to Herpes simplex Type 1 Neuronal Infection Leading to Encephalitis in Rat |
Non-retroviral RNA virus sequences ( NRVSs ) have been found in the chromosomes of vertebrates and fungi , but not plants . Here we report similarly endogenized NRVSs derived from plus- , negative- , and double-stranded RNA viruses in plant chromosomes . These sequences were found by searching public genomic sequence d... | Eukaryotic genomes contain sequences that have originated from DNA viruses and reverse-transcribing viruses , i . e . , retroviruses , pararetroviruses ( DNA viruses ) , and transposons . However , the sequences of non-retroviral RNA viruses , which are unable to convert their genomes to DNA , were until recently consi... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"plant",
"science",
"plant",
"evolution",
"virology",
"plant",
"pathogens",
"plant",
"biology",
"plant",
"pathology",
"biology",
"microbiology",
"viral",
"evolution"
] | 2011 | Widespread Endogenization of Genome Sequences of Non-Retroviral RNA Viruses into Plant Genomes |
The actin family of cytoskeletal proteins is essential to the physiology of virtually all archaea , bacteria , and eukaryotes . While X-ray crystallography and electron microscopy have revealed structural homologies among actin-family proteins , these techniques cannot probe molecular-scale conformational dynamics . He... | Simulations are a critical tool for uncovering the molecular mechanisms underlying biological form and function . Here , we use molecular-dynamics simulations to identify common and specific dynamical behaviors in four prokaryotic homologs of actin , a cytoskeletal protein that plays important roles in cellular structu... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"crystal",
"structure",
"monomers",
"condensed",
"matter",
"physics",
"geometry",
"mathematics",
"materials",
"science",
"protein",
"structure",
"crystallography",
"oligomers",
"polymer",
"chemistry",
"contractile",
"proteins",
"actins",
"solid",
"state",
"physics",
"prot... | 2019 | Conservation of conformational dynamics across prokaryotic actins |
Cutaneous leishmaniasis is caused by several Leishmania species that are associated with variable outcomes before and after therapy . Optimal treatment decision is based on an accurate identification of the infecting species but current methods to type Leishmania isolates are relatively complex and/or slow . Therefore ... | Cutaneous leishmaniasis is a disease due to a small parasite called Leishmania . This parasite causes disfiguring skin lesions that last for months or years . There are many different subtypes of Leishmania , each giving rise to lesions of different severity and responding to therapies in its own way . Treating physici... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"dermatology",
"medicine",
"and",
"health",
"sciences",
"clinical",
"research",
"design",
"synthetic",
"biology",
"immunology",
"microbiology",
"pediatrics",
"research",
"design",
"developmental",
"biology",
"clinical",
"medicine",
"global",
"health",
"veterinary",
"scien... | 2014 | Easy Identification of Leishmania Species by Mass Spectrometry |
Peroxiredoxins ( Prxs or Prdxs ) are a large protein superfamily of antioxidant enzymes that rapidly detoxify damaging peroxides and/or affect signal transduction and , thus , have roles in proliferation , differentiation , and apoptosis . Prx superfamily members are widespread across phylogeny and multiple methods hav... | Peroxiredoxins ( Prxs ) are a large , ubiquitous superfamily of proteins that are arguably the most important reductants of peroxide in biological systems . These proteins are involved in a diverse array of essential cellular functions , including peroxide reduction , signal transduction , circadian rhythms , chaperone... | [
"Abstract",
"Introduction",
"Results",
"and",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"taxonomy",
"database",
"searching",
"phylogenetics",
"data",
"management",
"protein",
"structure",
"sequence",
"motif",
"analysis",
"protein",
"structure",
"databases",
"sequence",
"similarity",
"searching",
"research",
"and",
"analysis",
"methods",
"sequence",
"analysis... | 2017 | An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins |
The plant hormone auxin regulates many aspects of plant growth and development . Recent progress in Arabidopsis provided a scheme that auxin receptors , TIR1/AFBs , target transcriptional co-repressors , AUX/IAAs , for degradation , allowing ARFs to regulate transcription of auxin responsive genes . The mechanism of au... | Auxin is an important plant hormone which regulates many aspects of plant growth and development , such as embryogenesis and directional growth in response to light or gravity . Recent molecular genetics advances in angiosperms revealed that transcriptional regulation is critical for auxin response . Although auxin res... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Auxin-Mediated Transcriptional System with a Minimal Set of Components Is Critical for Morphogenesis through the Life Cycle in Marchantia polymorpha |
Sex-specific traits that lead to the production of dimorphic gametes , sperm in males and eggs in females , are fundamental for sexual reproduction and accordingly widespread among animals . Yet the sex-biased genes that underlie these sex-specific traits are under strong selective pressure , and as a result of adaptiv... | While sexual reproduction is widespread among animals , it remains enigmatic to what extent sexual reproduction is conserved and when sex-specific gametogenesis ( spermatogenesis and oogenesis ) originated in animals . Here we demonstrate the presence of the reproductive-specific protein Boule throughout bilaterally-sy... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"evolutionary",
"biology/animal",
"genetics",
"evolutionary",
"biology/evolutionary",
"and",
"comparative",
"genetics",
"evolutionary",
"biology/sexual",
"behavior",
"genetics",
"and",
"genomics/disease",
"models",
"genetics",
"and",
"genomics/population",
"genetics",
"genetics... | 2010 | Widespread Presence of Human BOULE Homologs among Animals and Conservation of Their Ancient Reproductive Function |
Identifying genomic elements required for viability is central to our understanding of the basic physiology of bacterial pathogens . Recently , the combination of high-density mutagenesis and deep sequencing has allowed for the identification of required and conditionally required genes in many bacteria . Genes , howev... | The significant rise in drug resistant strains of Mycobacterium tuberculosis has highlighted the need for new drug targets . Here , we present a novel method of defining genetic elements required for optimal growth , a key first step for identifying potential drug targets . Similar strategies in other bacterial pathoge... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods",
"and",
"Materials"
] | [
"genome",
"analysis",
"tools",
"functional",
"genomics",
"genetic",
"screens",
"microbial",
"pathogens",
"biology",
"genomics",
"microbiology",
"microbial",
"growth",
"and",
"development",
"genetics",
"and",
"genomics"
] | 2012 | Global Assessment of Genomic Regions Required for Growth in Mycobacterium tuberculosis |
The appearance of the notochord represented a milestone in Deuterostome evolution . The notochord is necessary for the development of the chordate body plan and for the formation of the vertebral column and numerous organs . It is known that the transcription factor Brachyury is required for notochord formation in all ... | Transcription factors control where and when gene expression is switched on by binding to specific stretches of DNA known as cis-regulatory modules ( CRMs ) . In this study , we investigated the architecture and composition of CRMs that direct gene expression in the notochord—a transient rod-like structure found in all... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2013 | Functional Brachyury Binding Sites Establish a Temporal Read-out of Gene Expression in the Ciona Notochord |
Muscle morphogenesis is tightly coupled with that of motor neurons ( MNs ) . Both MNs and muscle progenitors simultaneously explore the surrounding tissues while exchanging reciprocal signals to tune their behaviors . We previously identified the Fat1 cadherin as a regulator of muscle morphogenesis and showed that it i... | Fat cadherins are evolutionarily conserved cell adhesion molecules , which play key roles in modulating tissue morphogenesis through the control of collective cell behavior and polarity . We previously identified the mouse Fat1 gene as a regulator of muscle morphogenesis and reported a role for this gene in muscle prog... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"medicine",
"and",
"health",
"sciences",
"nervous",
"system",
"population",
"genetics",
"neuroscience",
"gene",
"pool",
"developmental",
"biology",
"nerve",
"fibers",
"population",
"biology",
"embryos",
"immunologic",
"techniques",
"morphogenesis",
"research",
"and",
"a... | 2018 | Tissue-specific activities of the Fat1 cadherin cooperate to control neuromuscular morphogenesis |
B-cells not only produce immunoglobulins and present antigens to T-cells , but also additional key roles in the immune system . Current knowledge on the role of B-cells in infections caused by intracellular bacteria is fragmentary and contradictory . We therefore analysed the phenotypical and functional properties of B... | In infections with intracellular pathogens like Mycobacterium tuberculosis ( Mtb ) , B-cells have long been ignored as their primary product , immunoglobulins , are unlikely to recognize intracellular bacteria . However , we have analysed here the frequency , phenotype and function of B-cells in tuberculosis ( TB ) inf... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"blood",
"cells",
"innate",
"immune",
"system",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immune",
"physiology",
"cytokines",
"immunology",
"tropical",
"diseases",
"cloning",
"bacterial",
"diseases",
"developmental",
"biology",
"molecular",
"developme... | 2016 | Patients with Tuberculosis Have a Dysfunctional Circulating B-Cell Compartment, Which Normalizes following Successful Treatment |
To date , most genetic analyses of phenotypes have focused on analyzing single traits or analyzing each phenotype independently . However , joint epistasis analysis of multiple complementary traits will increase statistical power and improve our understanding of the complicated genetic structure of the complex diseases... | The widely used statistical methods test interaction for single phenotype . However , we often observe pleotropic genetic interaction effects . The simultaneous gene-gene ( GxG ) interaction analysis of multiple complementary traits will increase statistical power to detect GxG interactions . Although GxG interactions ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"genetic",
"networks",
"quantitative",
"trait",
"loci",
"variant",
"genotypes",
"quantitative",
"traits",
"genetic",
"mapping",
"epistasis",
"mathematics",
"statistics",
"(mathematics)",
"test",
"statistics",
"genome",
"analysis",
"network",
"analysis",
"research",
"and",... | 2016 | Functional Regression Models for Epistasis Analysis of Multiple Quantitative Traits |
P21 activated kinase ( PAK ) , PAK interacting exchange factor ( PIX ) , and G protein coupled receptor kinase interactor ( GIT ) compose a highly conserved signaling module controlling cell migrations , immune system signaling , and the formation of the mammalian nervous system . Traditionally , this signaling module ... | Cell migration is essential for the development and maintenance of metazoan tissue . A migrating cell must navigate through complex environments and properly interpret the signals present in its path . This cellular movement is accomplished through transduction of the signals into directed reorganization of the cellula... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"developmental",
"biology/morphogenesis",
"and",
"cell",
"biology",
"cell",
"biology/cell",
"signaling",
"cell",
"biology/morphogenesis",
"and",
"cell",
"biology",
"cell",
"biology/developmental",
"molecular",
"mechanisms",
"developmental",
"biology/molecular",
"development",
... | 2008 | A RAC/CDC-42–Independent GIT/PIX/PAK Signaling Pathway Mediates Cell Migration in C. elegans |
Several recent studies have shown a genetic influence on gene expression variation , including variation between the two chromosomes within an individual and variation between individuals at the population level . We hypothesized that genetic inheritance may also affect variation in chromatin states . To test this hypo... | Human health and disease are determined by an interaction between genetic background and environmental exposures . Both normal development and disease are mediated by epigenetic regulation of gene expression . The epigenetic regulation causes heritable changes in gene expression , which is not associated with DNA seque... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods",
"Supporting",
"Information"
] | [
"in",
"vitro",
"homo",
"(human)",
"genetics",
"and",
"genomics"
] | 2007 | Allele-Specific Chromatin Immunoprecipitation Studies Show Genetic Influence on Chromatin State in Human Genome |
Finding functional DNA binding sites of transcription factors ( TFs ) throughout the genome is a crucial step in understanding transcriptional regulation . Unfortunately , these binding sites are typically short and degenerate , posing a significant statistical challenge: many more matches to known TF motifs occur in t... | Identifying transcription factor ( TF ) binding sites across the genome is an important problem in molecular biology . Large-scale discovery of TF binding sites is usually carried out by searching for short DNA patterns that appear often within promoter regions of genes that are known to be co-bound by a TF . In such p... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"saccharomyces",
"computational",
"biology"
] | 2007 | A Nucleosome-Guided Map of Transcription Factor Binding Sites in Yeast |
Tsutsugamushi disease is an infectious disease transmitted to humans through the bite of the Orientia tsutsugamushi-infected chigger mite; however , host-pathogen interactions and the precise mechanisms of damage in O . tsutsugamushi infections have not been fully elucidated . Here , we analyzed the global metabolic ef... | Scrub typhus is an acute febrile illness caused by attacks of Orientia tsutsugamushi-carrying mites , and is the most prevalent febrile illness in the Asia-Pacific region . If not properly treated with antibiotics , patients often develop severe vasculitis that affects multiple organs , and the mortality rate can reach... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"biochemistry",
"metabolomics",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"host-pathogen",
"interactions",
"biology",
"and",
"life",
"sciences",
"pathogenesis",
"metabolism"
] | 2015 | Metabolic Responses to Orientia tsutsugamushi Infection in a Mouse Model |
The spatial organization of chromosomes within interphase nuclei is important for gene expression and epigenetic inheritance . Although the extent of physical interaction between chromosomes and their degree of compaction varies during development and between different cell-types , it is unclear how regulation of chrom... | The Cap-H2 condensin II subunit is required for interphase condensin II activity . Previous work has shown that low levels of Cap-H2 protein in interphase is achieved by SCFSlimb mediated protein turnover and limits chromatin-bound protein levels . Here we show that Casein Kinase I alpha ( CK1α ) is also a negative reg... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Drosophila Casein Kinase I Alpha Regulates Homolog Pairing and Genome Organization by Modulating Condensin II Subunit Cap-H2 Levels |
As data for microbial community structures found in various environments has increased , studies have examined the relationship between environmental labels given to retrieved microbial samples and their community structures . However , because environments continuously change over time and space , mixed states of some... | In the past decade , microbiomes from various natural and human symbiotic environments have been thoroughly studied . However , our knowledge is limited as to what types of environments affect the structure of a microbial community . In the first place , how can we define “environments” , in particular , the environmen... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"taxonomy",
"ecology",
"and",
"environmental",
"sciences",
"surface",
"water",
"microbiome",
"rivers",
"community",
"structure",
"microbiology",
"data",
"management",
"metagenomics",
"aquatic",
"environments",
"bodies",
"of",
"water",
"microbial",
"genomics",
"research",
... | 2018 | Latent environment allocation of microbial community data |
The giant non-fimbrial adhesin SiiE of Salmonella enterica mediates the first contact to the apical site of epithelial cells and enables subsequent invasion . SiiE is a 595 kDa protein composed of 53 repetitive bacterial immunoglobulin ( BIg ) domains and the only known substrate of the SPI4-encoded type 1 secretion sy... | The interaction of Salmonella enterica with polarized epithelial cells depends on the function of SiiE , a 595 kDa adhesin containing 53 repeats of a bacterial immunoglobulin ( BIg ) domain . SiiE is secreted and surface-expressed by a cognate type I secretion system ( T1SS ) . We found that BIg domains contain amino a... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"bacteriology",
"protein",
"transport",
"medicine",
"and",
"health",
"sciences",
"crystal",
"structure",
"pathology",
"and",
"laboratory",
"medicine",
"chemical",
"compounds",
"pathogens",
"cell",
"processes",
"condensed",
"matter",
"physics",
"microbiology",
"organic",
... | 2017 | Structural and functional dissection reveals distinct roles of Ca2+-binding sites in the giant adhesin SiiE of Salmonella enterica |
Environmental stressors can severely perturb cellular homeostasis and compromise viability . To cope with environmental stressors , eukaryotes have developed distinct signaling programs that allow for adaptation during different stress conditions . These programs often require a host of post-translational modifications... | The ability to sense and react to diverse environmental cues is a central aspect in the maintenance of cellular homeostasis . In response to harsh conditions , cells must rapidly deploy specific stress responses in order to adapt , survive , and proliferate . To ensure optimal spatial and temporal control over stress r... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"cellular",
"stress",
"responses",
"monomers",
"cell",
"processes",
"fungi",
"sumoylation",
"mapk",
"signaling",
"cascades",
"polymer",
"chemistry",
"stress",
"signaling",
"cascade",
"proteins",
"chemistry",
"yeast",
"biochemistry",
"signal",
"transduction",
"eukaryota",
... | 2019 | Osmolyte accumulation regulates the SUMOylation and inclusion dynamics of the prionogenic Cyc8-Tup1 transcription corepressor |
An important factor influencing the transmission dynamics of vector-borne diseases is the contribution of hosts with different parasitemia ( no . of parasites per ml of blood ) to the infected vector population . Today , estimation of this contribution is often impractical since it relies exclusively on limited-scale x... | An important factor influencing the transmission dynamics of vector-borne diseases is the contribution of hosts with different parasitemia ( no . of parasites per ml of blood ) to the infected vector population . In this study we developed a novel mechanistic model that facilitates the quantification of this contributi... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases",
"medicine",
"and",
"health",
"sciences",
"plant",
"science",
"emerging",
"infectious",
"diseases",
"infectious",
"disease",
"epidemiology",
"epidemiology",
"vector",
"biology",
"disease",
"dynamics",
"screening",
"guidelines",
"plant",
"pathology... | 2014 | Quantifying the Contribution of Hosts with Different Parasite Concentrations to the Transmission of Visceral Leishmaniasis in Ethiopia |
DNA sequences on X chromosomes often have a faster rate of evolution when compared to similar loci on the autosomes , and well articulated models provide reasons why the X-linked mode of inheritance may be responsible for the faster evolution of X-linked genes . We analyzed microarray and RNA–seq data collected from fe... | As species diverge over evolutionary time , they accumulate differences in the sequences of their genes and how those genes are expressed . We show that gene expression changes accumulate faster for genes on the X chromosome than for genes on the other chromosomes ( autosomes ) in Drosophila ( the “faster-X” effect ) .... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"genome",
"expression",
"analysis",
"genome",
"evolution",
"animal",
"models",
"drosophila",
"melanogaster",
"model",
"organisms",
"molecular",
"cell",
"biology",
"chromatin",
"chromosome",
"biology",
"gene",
"expression",
"comparative",
"genomics",
"biology",
"evolutiona... | 2012 | Faster-X Evolution of Gene Expression in Drosophila |
Natural populations exhibit a great deal of interindividual genetic variation in the response to toxins , exemplified by the variable clinical efficacy of pharmaceutical drugs in humans , and the evolution of pesticide resistant insects . Such variation can result from several phenomena , including variable metabolic d... | A striking feature of biology is that within populations there is substantial interindividual phenotypic variation for traits of biomedical significance . Some fraction of this variation is due to environmental factors , but for many traits segregating genetic differences contribute significantly to phenotypic variatio... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Identifying Loci Contributing to Natural Variation in Xenobiotic Resistance in Drosophila |
For directional movement , eukaryotic cells depend on the proper organization of their actin cytoskeleton . This engine of motility is made up of highly dynamic nonequilibrium actin structures such as flashes , oscillations , and traveling waves . In Dictyostelium , oscillatory actin foci interact with signals such as ... | The actin cytoskeleton of motile cells is comprised of highly dynamic structures . Recently , small oscillating actin foci have been discovered around the periphery of Dictyostelium cells . These oscillators are thought to enable pseudopod formation , but how their dynamics are regulated for this is unknown . Here , we... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"physiology",
"cell",
"motility",
"dictyosteliomycota",
"cell",
"polarity",
"model",
"organisms",
"cellular",
"structures",
"and",
"organelles",
"cytoskeleton",
"research",
"and",
"analysis",
"methods",
"contractile",
"proteins",
"actins",
"slime",
"molds",
"pro... | 2016 | Gβ Regulates Coupling between Actin Oscillators for Cell Polarity and Directional Migration |
The growth of scleractinian corals is strongly influenced by the effect of water motion . Corals are known to have a high level of phenotypic variation and exhibit a diverse range of growth forms , which often contain a high level of geometric complexity . Due to their complex shape , simulation models represent an imp... | A long-standing question in marine biology and coral biology is the morphological plasticity of corals , sponges and other marine sessile organisms and the influence of water movement . Usually branching species tend to develop symmetrical colonies where branches are being formed in all directions . There is a long sta... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"biophysic",
"al",
"simulations",
"marine",
"and",
"aquatic",
"sciences",
"biology",
"computational",
"biology",
"marine",
"biology"
] | 2013 | Modelling Growth and Form of the Scleractinian Coral Pocillopora verrucosa and the Influence of Hydrodynamics |
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